One of the really persistent issues in genomics is how to either get a list of things, or handle a list of things. or the overlap among the things. I think that was one of the most popular topics we dealt with in the early days of OpenHelix, but it’s still a issue that people need to handle in various ways. Some of the most interesting solutions have been various organism Venn diagrams, and the Rat Genome one is a classic, modeled here by Lior Pachter. I’m certain the need to list and organize genome features won’t go away. So when I saw that the RGD folks had another tool to offer ways to do this, I put it right in my list of upcoming tips. And then the draft post got buried under a list of other things I had to do. But I wanted to get back to it–so here is their step-by-step guide to the OLGA tool they offer, as this week’s Video Tip of the Week.
OLGA stands for: Object List Generator and Analyzer tool. Their newsletter announcement describes it in more details.
OLGA is a straightforward list builder for rat, human and mouse genes or QTLs, or rat strains, using any (or all) of a variety of querying options. The new tutorial video will walk you through the process of querying the RGD database using OLGA, including
- how to perform a simple query in OLGA
- how to further expand or filter your result set using additional criteria
- how to change your query parameters on the fly to refine your result set
- what options OLGA gives for analysis of your list once you have it.
You can get a list of items using various ontologies–maybe you want a specific type of receptor, for example, you can get a list of them. Or you can quickly create a list of genes in a certain genomic span. You can get the items that fall in a QTL. Or you can start with a list and get annotations. You can also look for overlaps among sets.
The video is a nice walk-through of how to construct your query and what you can access. One key feature is that it’s not just rat data as you might expect at RGD. Mouse and human data are also available.
You can create complex and clever queries, and link to all sorts of related data in very easy steps. Have a look at their resources, and their other videos for more help with different aspects of their collections.
RGD main site: http://rgd.mcw.edu/
OLGA directly: http://rgd.mcw.edu/rgdweb/generator/list.html
Shimoyama, M., De Pons, J., Hayman, G., Laulederkind, S., Liu, W., Nigam, R., Petri, V., Smith, J., Tutaj, M., Wang, S., Worthey, E., Dwinell, M., & Jacob, H. (2014). The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1026